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ELM->ATS coupling#4

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jbeisman wants to merge 73 commits intofmyuan:elm-devfmyuan/E3SM:elm-devfrom jbeisman:jb-ATSinterfacejbeisman/E3SM:jb-ATSinterfaceCopy head branch name to clipboard

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Commits on Feb 16, 2022

• Need to explicitly initialize 'budg_fluxG' for plev=p_inf (so-called 'all_time' integral fluxes), by default. Otherwise, it may cause budget checking err and model crash, for example, when ELM runs…

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• Modifying CNPBudgetMod error tolerance to be consistent with those in EcosystemBalanceCheckMod.

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• After rename 'clm' to 'elm', have to rename 'CLM_USRDAT' to 'ELM_USRDAT' as well. Otherwise, it fails to setup for '-res CLM_USRDAT', which must be '- res ELM_USRDAT'.

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Commits on Feb 21, 2022

• Machine File Modifications (1): add a locally user-defined Mac machine configuration, namely 'mymac', for using on Mac OSX.

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• Machine File Modifications (2a): Update machine configurations and inputdata directory for ORNL machine 'cades'.

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• Machine File Modifications (2b): Add a machine settings, MPILIBS=openmpi3, for CADES. It's software packages of AMANZI-TPLS for ATS, which are based on gcc/6.3.0 and openmpi-3.0.0. It's required to…

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• Machine File Modifications (2c): Add 'mpi-serial' for ELM on ORNL machine cades.

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• CPL_BYPASS modification (1): in case 'scale_factor' or 'add_offset' not in the input met data nc file, assign the former 1 and the latter 0 (i.e. no scaling of original dataset).

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• CPL_BYPASS modification (2): if v1 GSWP3 metdata for ICB, let the ending year be 2010.

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• CPL_BYPASS modification (3): adding a check for specific humidity.

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• CPL_BYPASS modification (4): a bug fix for CPL_BYPASS data load. The bug will crash model when restarting a run if the starting simulation year is beyond range of cycling forcing data period.

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• CPL_BYPASS modification (5): re-do CO2 import for CPL_BYPASS option - some missing in 'atm2lnd_vars'.

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• CPL_BYPASS modification (6): Fix an inconsistence of longitude format in CPL_BYPASS when calculating shortest distance between land grids.

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• CPL_BYPASS modification (7): Update GSWP3_daymet option for 'datm' mode, with GSWP3 v2 (1901-2014) downscaled by 1 km daymet v4 for Northern America dataset.

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Commits on Feb 25, 2022

• Add walltime and memory usage checking into CPL_BYPASS data loading.

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• Bugs in mosart - NO idea why it suddenly appears when building ELM with 'DEBUG' on.

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• GSWP3v2 is added as one option of 'DATM_MODE'.

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• The checking of grid-system in radians or degrees is only working for a globe, which NOT correct for partial globe (or region or point domains). So add an optional setting of mapping of grid unit -…

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• change datm's topo and presaero yearly extrapolating method.

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• A potential bug fix in CH4Mod.F90.

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• Hyperthreading on Summit appears to slow IO very much in ELM when with CPL_BYPASS.

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Commits on Apr 6, 2022

• Add a machine, 'wsl', Windows Subsystem for Linux for building/running ELM in wsl/ubuntu environments.

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• Add an example 'bashrc_wsl' to override $HOME/.bashrc, to port ELM model to WSL.

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• Add an example 'bashrc_gnu' to override $HOME/.bashrc, to port ELM model to mac osx.

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Commits on Jun 28, 2022

• GNU Fortran version >=10, for legacy fortran code it may require a flag: ' -fallow-argument-mismatch'

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• a BOZ bug for gcc version>=10.

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• Add openmpi to mymac's available mpilib.

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• EMI modifications for Alquimia, carried out by Ben Sulman.

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• CMake building settings for coupling ATS libraries into ELM.

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• ELM namelist addition for ATS coupling. This will add 3 namelists - use_ats, ats_inputdir, ats_inputfile.

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• Arbitrarily set saturated conductivity and porosity for bedrock bottom to very tiny values.

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• EMI modifications for ATS - 1st attempt.

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• EMI modifications for ATS - 10th attempt: v0

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• Add optional controls from ELM interface for ATS outputs.

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• in ATS, source (mass) is in negative (out of soils), and sink positive( into soil).

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• Let ATS interface run for one ELM time-step.

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• Allow ELM change ATS's starting time, when passing initial conditions.

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• In ATS, source-sink terms are in units of per m2 for surface water, but of per m3 for soil laers..

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• When coupling with ATS or PFLOTRAN, let init_cold water condition not dry. This is critical to frozen condition, under which otherwise it may take long to spinup.

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• bug fixes in CNPBudgetMod.F90. NOTE: it's fixed in later ELM version. The bug may only appear when restart and codes are compiled in DEBUG mode.

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• Initializing ATS flow PK's initial condition by ELM's ground water table, which corresponds to ATS water flow IC of hydraulic water head.

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• Let ELM hist_tape(0) control ATS vis output frequency.

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• When coupling with ATS, surface water inputs, named as 'gross_infiltration_soil', is pointed to net water onto surface, AND, 'gross_evap_soil' pointed to raw surface/soil evaporation. This is becau…

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• Total vegetation transpiration is as one of input to extract water from subsurface, alternative to vertically-distributed root water extraction. NOTE that only either of these two used in ATS (cann…

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Commits on Jun 29, 2022

• Additional terms for water Sources/Sinks from ELM to ATS.

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Commits on Jun 30, 2022

• Passing ATS water state variables to ELM.

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• At present, don't allow ATS simulated water states over-ride ELM's.

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Commits on Jul 1, 2022

• When ELM get data from ATS, 'water_content' and 'capillary_pressure_gas_liq' are passing, instead of 'saturation'. AND any unit conversion should be carried out in ATS interface, in order to avoid …

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Commits on Sep 26, 2022

• ats libraries updated.

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Commits on Sep 30, 2022

• wsl cmake changing.

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Commits on Oct 6, 2022

• EMI-ats writing control option bug - when ELM not writing out at all.

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Commits on Nov 2, 2022

• updates ATS API to match that on the ATS side

  

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• updates to ELM-ATS API based on team-code effort with Fengming and Ethan

  

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Commits on Nov 4, 2022

• Update EMI-ats codes after interface API changing.

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• Update EMI-ats libraries.

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Commits on Nov 14, 2022

• WSL machine files

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• Merge branch 'EMI-ats' of https://github.com/fmyuan/E3SM into EMI-ats

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Commits on Nov 22, 2022

• updates to ELM-ATS api -- for now assuming PFTs are consistent or set by ATS with 1 per grid cell

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Commits on Jan 17, 2023

• Merge branch 'EMI-ats' of https://github.com/fmyuan/E3SM into EMI-ats

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Commits on Jul 10, 2023

• update Fortran-C interface - WIP

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• updated generic EMI interface - WIP

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Commits on Aug 3, 2023

• updates to ATS interface and driver code

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• add a few new EMI variable enumerations

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• changes to data definition files

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• changes to data exchange files

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• cleanup some debugging statements

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• add modified HydrologyNoDrainage and config files specific to my system

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Commits on Aug 9, 2023

• Brought some new variables into EMI, created realively convenient patch filtering

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• Deactivate ELM subroutine Drainage() when running ATS; Make sure water balance variables are assigned values.

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• Getting closer - more cleanup, added some variables to EMI, etc.

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• Work toward full water balance accounting

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Commits on Aug 29, 2023

• Added environment file and shell script to aid in building examples.

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Commits on Oct 23, 2023

• Removes some stray comments and fixes a few assignments

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